Recently, I sent my D800 to Nikon for in-warranty repair of auto WB & AF problems.
I used the services of the repair department at Keeble & Shuchat in Palo Alto to work directly with Nikon. They wrote up the repair order, and sent the camera in for repair. (This is the store where I bought my D800.)
The camera came back last week, with cryptic notes from Nikon acknowledging AF & auto WB problems and their repair. I've only had time to run a few tests, but am happy to report that both AF & auto WB now seem to be performing well.
By using my local camera store's repair department services, I didn't have to deal directly with Nikon. The repair department acted on my behalf, making for a "no stress, no hassle" experience.
Thom's Comment: Good dealers will work to get an RMA from Nikon for something they sold you that had problems out of the box or under warranty. Sometimes you'll get a repair, as you did, sometimes they'll just swap out.